Linking ecology to genetics to better understand adaptation and evolution: a review in marine macrophytes

Ecological processes and intra-specific genetic diversity reciprocally affect each other. While the importance of uniting ecological variables and genetic variation to understand species’ plasticity, adaptation, and evolution is increasingly recognized, only few studies have attempted to address the intersection of population ecology and genetics using marine macrophyte as models. Representative empirical case studies on genetic diversity are reviewed that explore ecological and evolutionary processes in marine macrophytes. These include studies on environment-induced phenotypic plasticity and associated ecological adaptation; population genetic variation and structuring driven by ecological variation; and ecological consequences mediated by intraspecific and interspecific diversity. Knowledge gaps are also discussed that impede the connection of ecology and genetics in macrophytes and possible approaches to address these issues. Finally, an eco-evolutionary perspective is advocated, by incorporating structural-tofunctional genomics and life cycle complexity, to increase the understanding of the adaptation and evolution of macrophytes in response to environmental heterogeneity.info:eu-repo/semantics/publishedVersio

Effect of younger age on survival outcomes in T1N0M0 breast cancer: A propensity score matching analysis

Purpose We evaluated the effect of younger age on recurrence risk in Chinese women diagnosed with T1N0M0 breast cancer (BC), using propensity score matching (PSM) analysis. Methods We included 365 women who were diagnosed with T1N0M0 BC between 2003 and 2016, and who received surgery at our center. They were classified as younger (≤40 years) and older (>40 years). We used PSM to balance clinicopathologic characteristics between the two age groups. Survival was analyzed by the Kaplan–Meier method, before and after PSM. Results Over a median follow‐up period of 79 months, 54 patients developed recurrences. Before PSM, younger patients had worse recurrence‐free survival (RFS) than older patients. Significantly worse RFS was seen in younger patients with HER2+ BC compared with their older counterparts. Younger patients had higher rates of locoregional recurrence rather than metastasis, especially in the first 5 years after diagnosis. After PSM, the two age groups still significantly differed in 5‐year RFS. Conclusion Among PSM pairs with T1N0M0 BC, with equal baselines and treatment conditions, we found that patients who presented at younger ages had worse outcomes, independently of other pathological features. Younger patients with BC may require more individualized therapy to improve their prognosis

MtDNA-Based Phylogeography of the Red Alga Agarophyton vermiculophyllum (Gigartinales, Rhodophyta) in the Native Northwest Pacific

The repeated transgression and regression of coastlines mediated by the late Quaternary glacial–interglacial cycles make the northwest Pacific a hot spot to study marine speciation and population diversity. The red alga Agarophyton vermiculophyllum is an ecologically important species native to the northwest Pacific, capturing considerable research interest due to its wide-range invasiveness in Europe and North America. However, the knowledge of phylogeographic structure and intraspecific genetic diversity across the entire native range was still scarce. Here, we used 1,214-bp of mitochondrial cytochrome c oxidase subunit 1 (cox1) to explore phylogeographic patterns, lineage structure, and population genetic differentiation of 48 A. vermiculophyllum populations in the northwest Pacific. Our DNA data revealed overall high haplotype diversity and low nucleotide diversity and five phylogeographically structured genetic lineages that diverged significantly from each other. S-DIVA analysis showed the ancestors of A. vermiculophyllum originating from multiple areas encompassing the Japan–Pacific coast, East and South China Seas. This combined evidence indicates that A. vermiculophyllum might have survived in multiple scattered glacial refugia during the late Quaternary climate oscillations in the northwest Pacific. Such knowledge may help to better understand how palaeoclimate interacted with contemporary environments to contribute to intraspecific genetic variation and provide a new perspective for conserving natural resource of A. vermiculophyllum in the northwest Pacific

Study of J/ψ→ppˉJ/\psi\to p\bar{p} and J/ψ→nnˉJ/\psi\to n\bar{n}

The decays $J/\psi\to p\bar{p}$ and $J/\psi\to n\bar{n}$ have been investigated with a sample of 225.2 million $J/\psi$ events collected with the BESIII detector at the BEPCII $e^+e^-$ collider. The branching fractions are determined to be $\mathcal{B}(J/\psi\to p\bar{p})=(2.112\pm0.004\pm0.031)\times10^{-3}$ and $\mathcal{B}(J/\psi\to n\bar{n})=(2.07\pm0.01\pm0.17)\times10^{-3}$. Distributions of the angle $\theta$ between the proton or anti-neutron and the beam direction are well described by the form $1+\alpha\cos^2\theta$, and we find $\alpha=0.595\pm0.012\pm0.015$ for $J/\psi\to p\bar{p}$ and $\alpha=0.50\pm0.04\pm0.21$ for $J/\psi\to n\bar{n}$. Our branching-fraction results suggest a large phase angle between the strong and electromagnetic amplitudes describing the $J/\psi\to N\bar{N}$ decay.Comment: 16 pages, 13 figures, the 2nd version, submitted to PR

First observation of the M1 transition ψ(3686)→γηc(2S)\psi(3686)\to \gamma\eta_c(2S)

Using a sample of 106 million \psi(3686) events collected with the BESIII detector at the BEPCII storage ring, we have made the first measurement of the M1 transition between the radially excited charmonium S-wave spin-triplet and the radially excited S-wave spin-singlet states: \psi(3686)\to\gamma\eta_c(2S). Analyses of the processes \psi(2S)\to \gamma\eta_c(2S) with \eta_c(2S)\to \K_S^0 K\pi and K^+K^-\pi^0 gave an \eta_c(2S) signal with a statistical significance of greater than 10 standard deviations under a wide range of assumptions about the signal and background properties. The data are used to obtain measurements of the \eta_c(2S) mass (M(\eta_c(2S))=3637.6\pm 2.9_\mathrm{stat}\pm 1.6_\mathrm{sys} MeV/c^2), width (\Gamma(\eta_c(2S))=16.9\pm 6.4_\mathrm{stat}\pm 4.8_\mathrm{sys} MeV), and the product branching fraction (\BR(\psi(3686)\to \gamma\eta_c(2S))\times \BR(\eta_c(2S)\to K\bar K\pi) = (1.30\pm 0.20_\mathrm{stat}\pm 0.30_\mathrm{sys})\times 10^{-5}). Combining our result with a BaBar measurement of \BR(\eta_c(2S)\to K\bar K \pi), we find the branching fraction of the M1 transition to be \BR(\psi(3686)\to\gamma\eta_c(2S)) = (6.8\pm 1.1_\mathrm{stat}\pm 4.5_\mathrm{sys})\times 10^{-4}.Comment: 7 pages, 1 figure, 1 tabl

Two-photon widths of the χc0,2\chi_{c0, 2} states and helicity analysis for \chi_{c2}\ar\gamma\gamma}

Based on a data sample of 106 M $\psi^{\prime}$ events collected with the BESIII detector, the decays \psi^{\prime}\ar\gamma\chi_{c0, 2},\chi_{c0, 2}\ar\gamma\gamma are studied to determine the two-photon widths of the $\chi_{c0, 2}$ states. The two-photon decay branching fractions are determined to be {\cal B}(\chi_{c0}\ar\gamma\gamma) = (2.24\pm 0.19\pm 0.12\pm 0.08)\times 10^{-4} and {\cal B}(\chi_{c2}\ar\gamma\gamma) = (3.21\pm 0.18\pm 0.17\pm 0.13)\times 10^{-4}. From these, the two-photon widths are determined to be $\Gamma_{\gamma \gamma}(\chi_{c0}) = (2.33\pm0.20\pm0.13\pm0.17)$ keV, $\Gamma_{\gamma \gamma}(\chi_{c2}) = (0.63\pm0.04\pm0.04\pm0.04)$ keV, and $\cal R$ $=\Gamma_{\gamma \gamma}(\chi_{c2})/\Gamma_{\gamma \gamma}(\chi_{c0})=0.271\pm 0.029\pm 0.013\pm 0.027$, where the uncertainties are statistical, systematic, and those from the PDG {\cal B}(\psi^{\prime}\ar\gamma\chi_{c0,2}) and $\Gamma(\chi_{c0,2})$ errors, respectively. The ratio of the two-photon widths for helicity $\lambda=0$ and helicity $\lambda=2$ components in the decay \chi_{c2}\ar\gamma\gamma is measured for the first time to be $f_{0/2} =\Gamma^{\lambda=0}_{\gamma\gamma}(\chi_{c2})/\Gamma^{\lambda=2}_{\gamma\gamma}(\chi_{c2}) = 0.00\pm0.02\pm0.02$.Comment: 10 pages, 4 figure

Search for the Lepton Flavor Violation Process J/ψ→eμJ/\psi \to e\mu at BESIII

We search for the lepton-flavor-violating decay of the $J/\psi$ into an electron and a muon using $(225.3\pm2.8)\times 10^{6}$ $J/\psi$ events collected with the BESIII detector at the BEPCII collider. Four candidate events are found in the signal region, consistent with background expectations. An upper limit on the branching fraction of $\mathcal{B}(J/\psi \to e\mu)< 1.5 \times 10^{-7}$ (90% C.L.) is obtained

Search for Baryonic Decays of \psi(3770) and \psi(4040)

By analyzing data samples of 2.9 fb^{-1} collected at \sqrt s=3.773 GeV, 482 pb^{-1} collected at \sqrt s=4.009 GeV and 67 pb^{-1} collected at \sqrt s=3.542, 3.554, 3.561, 3.600 and 3.650 GeV with the BESIII detector at the BEPCII storage ring, we search for \psi(3770) and \psi(4040) decay to baryonic final states, including \Lambda\bar\Lambda\pi^+\pi^-, \Lambda \bar\Lambda\pi^0, \Lambda\bar\Lambda\eta, \Sigma^+ \bar\Sigma^-, \Sigma^0 \bar\Sigma^0, \Xi^-\bar\Xi^+ and \Xi^0\bar\Xi^0 decays. None are observed, and upper limits are set at the 90% confidence level.Comment: 9 pages, 3 figure

GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords

<p>Abstract</p> <p>Background</p> <p>Biomedical researchers often want to explore pathogenesis and pathways regulated by abnormally expressed genes, such as those identified by microarray analyses. Literature mining is an important way to assist in this task. Many literature mining tools are now available. However, few of them allows the user to make manual adjustments to zero in on what he/she wants to know in particular.</p> <p>Results</p> <p>We present our software program, GenCLiP (Gene Cluster with Literature Profiles), which is based on the methods presented by Chaussabel and Sher (<it>Genome Biol </it>2002, 3(10):RESEARCH0055) that search gene lists to identify functional clusters of genes based on up-to-date literature profiling. Four features were added to this previously described method: the ability to 1) manually curate keywords extracted from the literature, 2) search genes and gene co-occurrence networks related to custom keywords, 3) compare analyzed gene results with negative and positive controls generated by GenCLiP, and 4) calculate probabilities that the resulting genes and gene networks are randomly related. In this paper, we show with a set of differentially expressed genes between keloids and normal control, how implementation of functions in GenCLiP successfully identified keywords related to the pathogenesis of keloids and unknown gene pathways involved in the pathogenesis of keloids.</p> <p>Conclusion</p> <p>With regard to the identification of disease-susceptibility genes, GenCLiP allows one to quickly acquire a primary pathogenesis profile and identify pathways involving abnormally expressed genes not previously associated with the disease.</p